I am using trying to use the bulk upload template in CSV to upload 600+ records of fungi in Genus Cortinarius. I am planning a bulk sequencing project and want to add sequence data for these species.
However, the bulk upload tool keep rejecting my upload beause I do not have specific taxa name.
I work on a genus of fungi that is hard to ID, and many records have not good species guess beyond genus. This is allowed when I post single records on iNat. I am wondering what I am doing wrong in this upload or why it is not allowing me to upload with genus name only.
I can guess some random species for the 25% only to genus, but this is creating bad data and does not seem to align with our mission.
" translation missing: en.we_tried_to_process_your_upload_named_filename
The species listed below were not found in the iNaturalist database.
- Single taxon not found: Genus Cortinarius
- Row(s): 6, 7, 10, 12, 13, 15, 17, 19, 20
Please check the spelling for each entry. If your spelling is correct, search for the species at http://www.inaturalist.org/taxa/search. If the name is not yet in the iNaturalist database, you’ll need to add it before your bulk upload will work. Use the box at the bottom of the search page to import new names. If the name is present but applies to multiple valid taxa, try to use a more or less specific name that only matches a single taxon."
I’m not familiar with the bulk uploader, but maybe this is an issue with there also being a section Cortinarius and a subgenus Cortinarius and the uploader not being able to distinguish which the upload is for?
You have to use a name that only applies to one taxon, so if you resubmit them as “Webcaps” or “Cortinars” it will work because those names are not also on the subgenus or section.
Thank you for the suggestions. I will try this out and if it works it will definitely unblock my immediate process :) I assumed the taxon match was literal, not that it was doing some kind of matching against alternatives.
Unfortunately, this means I also cannot upload to SECTION as concepts like Dermocybe exist as both Sections and Subgenera in the taxon search.
Thanks for the help. I managed to upload over 550 observations. It was a little clunky with the various taxa issues but really helpful to understand the workaround.
It has also been a good quality control step for my own herbarium records as I found several typos, and generally updated the rigor of my records in the process.
Tip for others, I was careful to include a cross index to my personal herbarium records so I can also download and reindex my herbarium collection file with the inat numbers, and links for quick access to those photos.
If I get clever, as these are sequenced I would get someone to help me with a script that hacks this whole process into more of an off and online integrated relationship DB, to make my whole workflow easier.
Glad it’s working. If it’s at all helpful, here’s a script that pushes sequence data to an observation field: https://forum.inaturalist.org/t/how-to-bulk-batch-add-its-sequence-data-to-an-observation-field/31382
This script is great. I just looked it over and it makes sense.
However, ugh, I have started to review all the 500+ new observations and none of the geographical coordinates have translated into a location. I checked them again, and they are correctly formatted. It even threw errors on a few where I had another character.
On the observations the notes occur but not the actual co-ordinate.
Also, the geoprivacy did not work. Since the coords didn’t work, that’s not an issue but for a scaled upload this could be pretty critical.
Hm, I only see 137 that have locality notes but no coordinates and another 29 missing both coords and locality notes: https://www.inaturalist.org/observations?geo=false&geoprivacy=open&user_id=sulcatus&verifiable=any
When you uploaded, did you only give the description of the location, or did you also give the lat/lon coordinates?
Can you paste in a few lines from your csv that didn’t go as expected?
Ah, this is encouraging. I am still learning how to navigate at scale :) I checked and now realize I’m the one who made the error.
I had broken the file into two - one in which I had updated all fields with coords and location data, and one in which I had not. Unfortunately, when fixing errors in taxa I inadvertantly uploaded the full file. This means those I planned to work on next are up too (without the right geoprivacy and/or locations).
Sigh, well we live and learn. I can manage to fix these over time.